AbstractTyphoons frequently induce algal blooms in the open ocean based on the satellite remote sensing data. However, the effects of typhoons on nearshore areas are not fully clarified due to the inaccessibility of in situ sampled data and the low accuracy of satellite data in the nearshore areas. To understand the biogeochemical and ecological changes in semi‐enclosed bays under the influence of typhoons, physicochemical parameters and isotopic compositions of surface water were measured in Zhanjiang Bay during the super Typhoon Mujigae and nontyphoon periods. The results show that the chlorophyll a (Chl a) concentrations inside and outside the bay during these two periods were considerably different. During typhoon periods, the positive apparent oxygen utilization and unsaturated dissolved oxygen (DO) values suggested significant biological degradation in Zhanjiang Bay, rather than the algal blooms reported by previous studies. In contrast, during nontyphoon periods, particulate organic matter (POM: POC and PN) was mainly generated by in situ phytoplankton production, as indicated by a low POC/Chl a ratio (<99), low C/N ratio, and positive correlations between PN, POC, and Chl a. Isotopic analysis of the particulate N (PN) and nitrate (NO3−) indicated that the 15N‐enriched PN in both periods originally came from sewage‐dissolved inorganic N. These results suggest that the typhoon‐induced decomposition processes, rather than algal blooms, in this semi‐enclosed bay in the northern South China Sea, providing new understanding of the impact of the typhoons on marine biogeochemistry and ecology.